rs10491650

Variant names:

• chr9-5203054-T-C
• rs10491650

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.296 in 152,052 control chromosomes in the GnomAD database, including 6,787 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (6787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44997 AN: 151934 Hom.: 6780 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.291

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.296 AC: 45047 AN: 152052 Hom.: 6787 Cov.: 32 AF XY: 0.301 AC XY: 22363 AN XY: 74342

African (AFR) AF: 0.330 AC: 13668 AN: 41464

American (AMR) AF: 0.284 AC: 4334 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3472

East Asian (EAS) AF: 0.257 AC: 1329 AN: 5178

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4812

European-Finnish (FIN) AF: 0.352 AC: 3716 AN: 10568

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18561 AN: 67956

Other (OTH) AF: 0.292 AC: 618 AN: 2114

Alfa AF: 0.297 Hom.: 1165

Bravo AF: 0.288

Asia WGS AF: 0.312 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.80
PhyloP100		-1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10491650; hg19: chr9-5203054; COSMIC: COSV60323497;